Pokemon may resemble animals or plants (or even goddamned lawn mowers), but they all intertwine into a single breeding population, meaning they're technically one big species. They're like different breeds of dog, if dogs came shaped like centipedes, dinosaurs, or ice cream. So, the Earth is populated by a single ultimate mega-species that has chosen to imitate an entire ecosystem of curiously absent creatures.
Pokemon Seem Intelligently Designed
Pokemon are suspiciously user-friendly, despite their catastrophic powers and feral appearance. They enjoy being tamed by humans, they have to be forced into battle against each other to evolve and grow, and, most bizarrely, they're compatible with electronics. They can be stored and uploaded as computer data. Combat-oriented, domestication-ready, downloadable life forms generally don't occur in the natural world, which suggests that the Pokemon are products of biological engineering. However, people clearly don't have a fucking clue where they came from, which brings us to our next point ...